VFDB 2008 release: an enhanced web-based resource for comparative pathogenomics

被引：125

作者：

Yang, Jian ^{[1
]}

Chen, Lihong ^{[1
,2
]}

Sun, Lilian ^{[1
]}

Yu, Jun ^{[3
]}

Jin, Qi ^{[1
,2
]}

机构：

[1] Chinese Ctr Dis Control & Prevent, Natl Inst Viral Dis Control & Prevent, State Key Lab Mol Virol & Genet Engn, Beijing 100176, Peoples R China

[2] Chinese Acad Med Sci, Inst Pathogen Biol, Beijing 100730, Peoples R China

[3] Univ Strathclyde, Strathclyde Inst Pharm & Biomed Sci, Glasgow G1 1XW, Lanark, Scotland

来源：

NUCLEIC ACIDS RESEARCH | 2008年 / 36卷

基金：

中国国家自然科学基金;

关键词：

D O I：

10.1093/nar/gkm951

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

Virulence factor database (VFDB) was set up in 2004 dedicated for providing current knowledge of virulence factors (VFs) from various medical significant bacterial pathogens to facilitate pathogenomic research. Nowadays, complete genome sequences of almost all the major pathogenic microbes have been determined, which makes comparative genomics a powerful approach for uncovering novel virulence determinants and hidden aspects of pathogenesis. VFDB was therefore upgraded to present the enormous diversity of bacterial genomes in terms of virulence genes and their organization. The VFDB 2008 release includes the following new features; (i) detailed tabular comparison of virulence composition of a given genome with other genomes of the same genus, (ii) multiple alignments and statistical analysis of homologous VFs and (iii) graphical comparison of genomic organizations of virulence genes. Comparative analysis of the numerous VFs will improve our understanding of the nature and evolution of virulence, as well as the development of new therapeutic and preventive strategies. VFDB 2008 release offers more user-friendly tools for comparative pathogenomics and it is publicly accessible at http://www.mgc.ac.cn/VFs/.

引用

页码：D539 / D542

页数：4

共 10 条

[1] Gapped BLAST and PSI-BLAST: a new generation of protein database search programs [J].

Altschul, SF ;

Madden, TL ;

Schaffer, AA ;

Zhang, JH ;

Zhang, Z ;

Miller, W ;

Lipman, DJ .

NUCLEIC ACIDS RESEARCH, 1997, 25 (17) :3389-3402

[2] Infectious diseases - A global challenge [J].

Becker, Katja ;

Hu, Ying ;

Biller-Andorno, Nikola .

INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY, 2006, 296 (4-5) :179-185

[3] VFDB: a reference database for bacterial virulence factors [J].

Chen, LH ;

Yang, J ;

Yu, J ;

Ya, ZJ ;

Sun, LL ;

Shen, Y ;

Jin, Q .

NUCLEIC ACIDS RESEARCH, 2005, 33 :D325-D328

[4] Haemophilus influenzae:: Genetic variability and natural selection to identify virulence factors [J].

Gilsdorf, JR ;

Marrs, CF ;

Foxman, B .

INFECTION AND IMMUNITY, 2004, 72 (05) :2457-2461

[5] Pathogenomics of Listeria spp. [J].

Hain, Torsten ;

Chatterjee, Som S. ;

Ghaia, Rohit ;

Kuenne, Carsten Tobias ;

Billion, Andre ;

Steinweg, Christiane ;

Domann, Eugen ;

Kaerst, Uwe ;

Jaensch, Lothar ;

Wehland, Jurgen ;

Eisenreich, Wolfgang ;

Bacherc, Adelbert ;

Joseph, Biju ;

Schaer, Jennifer ;

Kreft, Jurgen ;

Klumpp, Jochen ;

Loessner, Martin J. ;

Dorscht, Julia ;

Neuhaus, Klaus ;

Fuchs, Thilo M. ;

Scherer, Siegfried ;

Doumith, Michel ;

Jacquet, Christine ;

Martin, Paul ;

Cossart, Pascale ;

Rusniock, Christophe ;

Glaser, Philippe ;

Buchrieser, Carmen ;

Goebel, Werner ;

Chakraborty, Trinad .

INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY, 2007, 297 (7-8) :541-557

[6] Microbial genome evolution: sources of variability [J].

Mira, A ;

Klasson, L ;

Andersson, SGE .

CURRENT OPINION IN MICROBIOLOGY, 2002, 5 (05) :506-512

[7] NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins [J].

Pruitt, Kim D. ;

Tatusova, Tatiana ;

Maglott, Donna R. .

NUCLEIC ACIDS RESEARCH, 2007, 35 :D61-D65

[8] CLUSTAL-W - IMPROVING THE SENSITIVITY OF PROGRESSIVE MULTIPLE SEQUENCE ALIGNMENT THROUGH SEQUENCE WEIGHTING, POSITION-SPECIFIC GAP PENALTIES AND WEIGHT MATRIX CHOICE [J].

THOMPSON, JD ;

HIGGINS, DG ;

GIBSON, TJ .

NUCLEIC ACIDS RESEARCH, 1994, 22 (22) :4673-4680

[9] Genome dynamics and diversity of Shigella species, the etiologic agents of bacillary dysentery [J].

Yang, F ;

Yang, J ;

Zhang, XB ;

Chen, LH ;

Jiang, Y ;

Yan, YL ;

Tang, XD ;

Wang, J ;

Xiong, ZH ;

Dong, J ;

Xue, Y ;

Zhu, YF ;

Xu, XY ;

Sun, LL ;

Chen, SX ;

Nie, H ;

Peng, JP ;

Xu, JG ;

Wang, Y ;

Yuan, ZH ;

Wen, YM ;

Yao, ZJ ;

Shen, Y ;

Qiang, BQ ;

Hou, YD ;

Yu, J ;

Jin, Q .

NUCLEIC ACIDS RESEARCH, 2005, 33 (19) :6445-6458

[10] ShiBASE:: an integrated database for comparative genomics of Shigella [J].

Yang, Jian ;

Chen, Lihong ;

Yu, Jun ;

Sun, Lilian ;

Jin, Qi .

NUCLEIC ACIDS RESEARCH, 2006, 34 :D398-D401

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